This might be a long shot, but I had something similar with Fallout 3 and that little Windows Gadgets thingy popping through. Might be worth trying to disable any Widgets, Gadgets, doo-dads, etc.
Running XP with no such widgets, gadgets, or thingys.

It seems to happen when the frame rate gets taxed. Like approaching a settlement or when a bunch of landscape gets drawn as you approach it.
PS: I said "right side" but I meant "left side". I should probably drink more coffee before posting...